Glycoside Hydrolase Family 57 - Revision history

Eduardo Moreno Prieto at 10:08, 26 February 2024

2024-02-26T10:08:53Z

Stefan Janecek at 11:37, 5 February 2024

2024-02-05T11:37:26Z

Stefan Janecek at 11:34, 5 February 2024

2024-02-05T11:34:51Z

Stefan Janecek at 11:33, 5 February 2024

2024-02-05T11:33:51Z

Stefan Janecek at 11:29, 5 February 2024

2024-02-05T11:29:26Z

Stefan Janecek at 11:28, 5 February 2024

2024-02-05T11:28:15Z

Stefan Janecek at 11:23, 5 February 2024

2024-02-05T11:23:30Z

Stefan Janecek at 11:18, 5 February 2024

2024-02-05T11:18:13Z

Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

2021-12-18T21:18:35Z

Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

Stefan Janecek at 17:32, 2 July 2014

2014-07-02T17:32:20Z

@@ Line 11: / Line 11: @@
 |-
 |'''Clan'''
-|GH-S
+|GH-T
 |-
 |'''Mechanism'''

@@ Line 84: / Line 84: @@
 #Laderman1993b pmid=8226989
 #Janecek2012 pmid=22819817
-#Polacek2023 Polacek A, Janecek S. "Sequence-structural features and evolution of the α-amylase family GH119 revealed by the in silico analysis of its relatedness to the family GH57." Biologia 2023; 78(7), 1847-60. [https://doi.org/10.1007/s11756-023-01349-y DOI: 10.1007/s11756-023-01349-y]
+#Polacek2023 Polacek A, Janecek S. ''Sequence-structural features and evolution of the α-amylase family GH119 revealed by the in silico analysis of its relatedness to the family GH57.'' Biologia 2023; 78(7): 1847-60. [https://doi.org/10.1007/s11756-023-01349-y DOI: 10.1007/s11756-023-01349-y]
 #Vuillemin2024 pmid=38280706
 #Palomo2011 pmid=21097495
 #Imamura2003 pmid=12618437
 #Imamura2001 pmid=11591160
@@ Line 96: / Line 94: @@
 #Kang2005 pmid=15599521
 #Murakami2006 pmid=16885460
-#Janecek2005 Janecek S ''Amylolytic families of glycoside hydrolases: focus on the family GH-57.'' Biologia 2005; 60(Suppl. 16) 177-84. ([http://biologia.savba.sk/Suppl_16/Janecek_S.pdf PDF])
+#Janecek2005 Janecek S ''Amylolytic families of glycoside hydrolases: focus on the family GH-57.'' Biologia 2005; 60(Suppl. 16): 177-84. ([http://biologia.savba.sk/Suppl_16/Janecek_S.pdf PDF])
-#vanLieshout2003 van Lieshout JFT, Verhees CH, Ettema TJG, van der Saar S, Imamura H, Matsuzawa H, van der Oost J, de Vos WM. ''Identification and molecular characterization of a novel type of α-galactosidase from Pyrococcus furiosus.'' Biocatal Biotransform 2003; 21(4-5) 243-52. ([http://dx.doi.org/10.1080/10242420310001614342 DOI: 10.1080/10242420310001614342])
+#vanLieshout2003 van Lieshout JFT, Verhees CH, Ettema TJG, van der Saar S, Imamura H, Matsuzawa H, van der Oost J, de Vos WM. ''Identification and molecular characterization of a novel type of α-galactosidase from Pyrococcus furiosus.'' Biocatal Biotransform 2003; 21(4-5): 243-52. [http://dx.doi.org/10.1080/10242420310001614342 DOI: 10.1080/10242420310001614342])
 #Dickmanns2006 pmid=16510973
 #Santos2011 pmid=21104698

@@ Line 35: / Line 35: @@
 It is worth mentioning that the two founding members, i.e. the “α-amylases” from ''Dictyoglomus thermophilum'' and ''Pyrococcus furiosus'' are 4-α-glucanotransferases; the former was proven to have transglycosylating activity <cite>Nakajima2004</cite>, whereas the latter was already known to exhibit also the 4-α-glucanotransferase activity <cite>Laderman1993b</cite>.
-A detailed in silico prediction study has indicated a close relatedness of family GH57 to the family GH119 concerning catalytic domain fold, catalytic machinery and conserved sequence regions <cite>Janecek2012</cite>. This original prediction has recently been updated using the AlphFold-generated structural model of a GH119 representative <cite>Polacek2023</cite> and finally confirmed also experimentally by the biochemical characterization of five GH119 members exhibiting a single α-amylase specificity but distinct product profile <cite>Vuillemin2024<cite>.
+A detailed in silico prediction study has indicated a close relatedness of family GH57 to the family GH119 concerning catalytic domain fold, catalytic machinery and conserved sequence regions <cite>Janecek2012</cite>. This original prediction has recently been updated using the AlphFold-generated structural model of a GH119 representative <cite>Polacek2023</cite> and finally confirmed also experimentally by the biochemical characterization of five GH119 members exhibiting a single α-amylase specificity but distinct product profile <cite>Vuillemin2024</cite>.
 == Kinetics and Mechanism ==

@@ Line 35: / Line 35: @@
 It is worth mentioning that the two founding members, i.e. the “α-amylases” from ''Dictyoglomus thermophilum'' and ''Pyrococcus furiosus'' are 4-α-glucanotransferases; the former was proven to have transglycosylating activity <cite>Nakajima2004</cite>, whereas the latter was already known to exhibit also the 4-α-glucanotransferase activity <cite>Laderman1993b</cite>.
-A detailed in silico prediction study has indicated a close relatedness of family GH57 to the family GH119 concerning catalytic domain fold, catalytic machinery and conserved sequence regions <cite>Janecek2012</cite>. This original prediction has recently been updated <cite>Polacek2023</cite> and finally confirmed by experimental characterization of the
+A detailed in silico prediction study has indicated a close relatedness of family GH57 to the family GH119 concerning catalytic domain fold, catalytic machinery and conserved sequence regions <cite>Janecek2012</cite>. This original prediction has recently been updated using the AlphFold-generated structural model of a GH119 representative <cite>Polacek2023</cite> and finally confirmed also experimentally by the biochemical characterization of five GH119 members exhibiting a single α-amylase specificity but distinct product profile <cite>Vuillemin2024<cite>.
 == Kinetics and Mechanism ==
@@ Line 85: / Line 85: @@
 #Janecek2012 pmid=22819817
 #Polacek2023 Polacek A, Janecek S. "Sequence-structural features and evolution of the α-amylase family GH119 revealed by the in silico analysis of its relatedness to the family GH57." Biologia 2023; 78(7), 1847-60. [https://doi.org/10.1007/s11756-023-01349-y DOI: 10.1007/s11756-023-01349-y]
 #Palomo2011 pmid=21097495
 #Imamura2003 pmid=12618437
 #Imamura2001 pmid=11591160

@@ Line 84: / Line 84: @@
 #Laderman1993b pmid=8226989
 #Janecek2012 pmid=22819817
 #Polacek2023 Polacek A, Janecek S. "Sequence-structural features and evolution of the α-amylase family GH119 revealed by the in silico analysis of its relatedness to the family GH57." Biologia 2023; 78(7), 1847-60. [https://doi.org/10.1007/s11756-023-01349-y DOI: 10.1007/s11756-023-01349-y]
 #Palomo2011 pmid=21097495
 #Imamura2003 pmid=12618437
 #Imamura2001 pmid=11591160

@@ Line 1: / Line 1: @@
 {{CuratorApproved}}
-* [[Author]]: ^^^Stefan Janecek^^^
+* [[Author]]: [[User:Stefan Janecek|Stefan Janecek]]
-* [[Responsible Curator]]:  ^^^Stefan Janecek^^^
+* [[Responsible Curator]]:  [[User:Stefan Janecek|Stefan Janecek]]
 ----

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 The family has expanded mainly due to the results of genome sequencing projects. More than a thousand of members are known <cite>Cantarel2009,Lombard2014</cite>, all from prokaryotes (with ~1:4 ratio for Archaea:Bacteria) <cite>Blesak2012</cite>. The enzyme specificities of family GH57 includes α-amylase (EC [{{EClink}}3.2.1.1 3.2.1.1]), α-galactosidase (EC [{{EClink}}3.2.1.22 3.2.1.22]), amylopullulanase (EC [{{EClink}}3.2.1.41 3.2.1.41]), branching enzyme (EC [{{EClink}}2.4.1.18 2.4.1.18]) and 4-α-glucanotransferase (EC [{{EClink}}2.4.1.25 2.4.1.25]).
-An archaeal GH57 amylopullulanase from ''Staphylothermus marinus'' has been described exhibiting also the activity of cyclodextrinase (EC [{{EClink}}3.2.1.54 3.2.1.54]) <cite>Li2014</cite>. Based on a preliminary observation that the PF0870 protein encoded in the ''Pyrococcus furiosus'' genome produced maltose <cite>Comfort2008</cite>, a group of GH57 members with proposed specificity of maltogenic amylase (EC [{{EClink}}3.2.1.133 3.2.1.133]) was predicted <cite>Blesak2013</cite> together with another group of non-specified amylases following the partial characterization of an amylolytic enzyme from an uncultured bacterium <cite>Wang2011</cite>. The maltogenic specificity (or maltose-forming amylase) has already been definitively confirmed by both biochemical <cite>Jung2014,Jeon2014</cite> and structural <cite>Park2014</cite> studies. The family GH57 contains further a group of probably non-enzymatic members, i.e. the so-called α-amylase-like proteins having a substitution in one or both catalytic residues <cite>Janecek2011</cite>.
+An archaeal GH57 amylopullulanase from ''Staphylothermus marinus'' has been described exhibiting also the activity of cyclodextrinase (EC [{{EClink}}3.2.1.54 3.2.1.54]) <cite>Li2013</cite>. Based on a preliminary observation that the PF0870 protein encoded in the ''Pyrococcus furiosus'' genome produced maltose <cite>Comfort2008</cite>, a group of GH57 members with proposed specificity of maltogenic amylase (EC [{{EClink}}3.2.1.133 3.2.1.133]) was predicted <cite>Blesak2013</cite> together with another group of non-specified amylases following the partial characterization of an amylolytic enzyme from an uncultured bacterium <cite>Wang2011</cite>. The maltogenic specificity (or maltose-forming amylase) has already been definitively confirmed by both biochemical <cite>Jung2014,Jeon2014</cite> and structural <cite>Park2014</cite> studies. The family GH57 contains further a group of probably non-enzymatic members, i.e. the so-called α-amylase-like proteins having a substitution in one or both catalytic residues <cite>Janecek2011</cite>.
 It is worth mentioning that the two founding members, i.e. the “α-amylases” from ''Dictyoglomus thermophilum'' and ''Pyrococcus furiosus'' are 4-α-glucanotransferases; the former was proven to have transglycosylating activity <cite>Nakajima2004</cite>, whereas the latter was already known to exhibit also the 4-α-glucanotransferase activity <cite>Laderman1993b</cite>.